[Genome] request for hg18 to hg16

Tue Apr 1 18:59:28 PDT 2008

Thanks a lot for the quick reply.
Please have a look at the attached snapshot of my liftOver session.
I am not sure where am I going wrong. I have tried several different
formats, but the program never recognized the files. The files were
definitely there as I could open them using other applications.

I had also ensured that the data is in the recommended BED format.

Thanks again for your help.
Regards,
Ashutosh.

PS: Also, I notice that you are just typing liftOver from the command
promt, which never worked for me. I always got the error-"command not
found". So I had to use the strategy as in the attached file. Is there
some problem with the installation of the file? I am a windows user &
relatively new to mac/unix system.

-----Original Message-----
From: Brooke Rhead [mailto:rhead at soe.ucsc.edu] 
Sent: Tuesday, April 01, 2008 8:30 PM
To: Gupta, Ashutosh (NIH/NCI) [F]
Cc: genome at soe.ucsc.edu
Subject: Re: [Genome] request for hg18 to hg16

Hi Ashutosh,

What kind of problem are you experiencing?

If you just need instructions on how to use the command-line tool, you 
can run the liftOver command with no arguments to see instructions.  It 
should look something like this:

-----
$ liftOver

liftOver - Move annotations from one assembly to another
usage:
    liftOver oldFile map.chain newFile unMapped
oldFile and newFile are in bed format by default, but can be in GFF and
maybe eventually others with the appropriate flags below.
The map.chain file has the old genome as the target and the new genome
as the query.

***********************************************************************
WARNING: liftOver was only designed to work between different
          assemblies of the same organism, it may not do what you want
          if you are lifting between different organisms.
***********************************************************************

options:
    -minMatch=0.N Minimum ratio of bases that must remap. Default 0.95
    -gff  File is in gff/gtf format.  Note that the gff lines are
converted
          separately.  It would be good to have a separate check after
this
          that the lines that make up a gene model still make a 
plausible gene
          after liftOver
    -genePred - File is in genePred format
    -sample - File is in sample format
    -bedPlus=N - File is bed N+ format
    -positions - File is in browser "position" format
    -hasBin - File has bin value (used only with -bedPlus)
    -tab - Separate by tabs rather than space (used only with -bedPlus)
    -pslT - File is in psl format, map target side only
    -minBlocks=0.N Minimum ratio of alignment blocks/exons that must map
                   (default 1.00)
    -fudgeThick    If thickStart/thickEnd is not mapped, use the closest
                   mapped base.  Recommended if using -minBlocks.
    -multiple               Allow multiple output regions
    -minChainT, -minChainQ  Minimum chain size in target/query, when
mapping
                            to multiple output regions (default 0, 0)
    -minSizeT               deprecated synonym for -minChainT (ENCODE 
compat.)
    -minSizeQ               Min matching region size in query with 
-multiple.
    -chainTable             Used with -multiple, format is db.tablename,
                                to extend chains from net (preserves
dups)
    -errorHelp              Explain error messages

-----

If you are only converting 50 positions from hg18 to hg16, it might be 
easier to use the web-based tool, as Kayla suggested.  (Or did I 
misunderstand your original question, and you need to convert many more 
than 50 positions?)

--
Brooke Rhead
UCSC Genome Bioinformatics Group

Gupta, Ashutosh (NIH/NCI) [F] wrote:
> Hi, 
> 
> I am having problem with conversions across different builds.
> 
> I have the liftOver tool for Mac OS X & all the relevant chain files.
> 
> Any help on this would be appreciated.
> 
> Thanks,
> 
> Ashutosh.
> 
> -----Original Message-----
> From: Kayla Smith [mailto:kayla at soe.ucsc.edu] 
> Sent: Monday, March 24, 2008 5:15 PM
> To: Gupta, Ashutosh (NIH/NCI) [F]
> Cc: genome at soe.ucsc.edu
> Subject: Re: [Genome] request for hg18 to hg16
> 
> 
> Hello Ashutosh,
> 
> You can use our online liftOver tool to convert from hg18 to hg17, and

> then from hg17 to hg16.  Here is the link:
> http://genome.ucsc.edu/cgi-bin/hgLiftOver
> 
> See this FAQ on downloading our source:
> http://genome.ucsc.edu/FAQ/FAQdownloads#download27
> 
> I hope this information is helpful to you.  Please don't hesitate to 
> contact us again if you require further assistance.
> 
> Kayla Smith
> UCSC Genome Bioinformatics Group
> 
> 
> Gupta, Ashutosh (NIH/NCI) [F] wrote:
>> Hi,
>>
>> Would it be possible to get a liftover file for conversion from hg18
> to
>> hg16?
>>
>> Also, is there any windows based conversion mechanism? I need to
> convert
>> about 50 nimblegen encode array hybridization, a windows based tool
>> would be very helpful.
>>
>> Even the conversion source code in C (or in Mathematica or Matlab)
> would
>> be very helpful. 
>>
>> Thanks,
>>
>> Ashutosh.
>>
>>  
>>
>> PS: I can also help develop a tool for windows system, depends on
>> complexity & time though. I am sure a lot of people would find it
>> useful.
>>
>> _______________________________________________
>> Genome maillist  -  Genome at soe.ucsc.edu
>> http://www.soe.ucsc.edu/mailman/listinfo/genome
> 
> 
> _______________________________________________
> Genome maillist  -  Genome at soe.ucsc.edu
> http://www.soe.ucsc.edu/mailman/listinfo/genome